The distribution of human genetic diversity: A comparison of mitochondrial, autosomal, and Y-chromosome data

American Journal of Human Genetics

Volumn 66, Issue 3, 2000, Pages 979-988

  Jorde, Lynn B ^a   Watkins, W S ^a   Bamshad, M J ^b   Dixon, M E ^a   Ricker, C E ^a   Seielstad, M T ^c   Batzer, M A ^d  

^a UNIVERSITY OF UTAH HEALTH SCIENCES CENTER   (United States)

^b UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^c HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^d LOUISIANA STATE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

ALLELE; ARTICLE; DNA SEQUENCE; GENETIC DRIFT; GENETIC POLYMORPHISM; HUMAN; POPULATION GENETICS; PRIORITY JOURNAL; TANDEM REPEAT; Y CHROMOSOME;

EID: 0033912515     PISSN: 00029297     EISSN: None     Source Type: Journal    
DOI: 10.1086/302825     Document Type: Article

References (75)

1. Arcot SS, Adamson AW, Lamerdin JE, Kanagy B, Deininger PL, Carrano AV, Batzer MA (1996) Alu fossil relics - distribution and insertion polymorphism. Genome Res 6: 1084-1092
2. Arcot SS, Adamson AW, Risch G, LaFleur J, Lamerdin JE, Carrano AV, Batzer MA (1998) High-resolution cartography of recently integrated chromosome 19-specific Alu fossils. J Mol Biol 281:843-855
3. Arcot SS, DeAngelis MM, Sherry ST, Adamson AW, Lamerdin JE, Deininger PL, Carrano AV, et al (1997) Identification and characterization of two polymorphic Ya5 Alu repeats. Mutat Res 382:5-11
4. Bamshad MJ, Watkins WS, Dixon ME, Rao BB, Naidu JM, Prasad BVR, Reddy PG, et al (1998) Female gene flow stratifies Hindu castes. Nature 395:651-652
5. Barbujani G, Magagni A, Minch E, Cavalli-Sforza LL (1997) An apportionment of human DNA diversity. Proc Natl Acad Sci USA 94:4516-4519
6. Batzer MA, Stoneking M, Alegria-Hartman M, Bazan H, Kass DH, Shaikh TH, Novick GE, et al (1994) African origin of human-specific polymorphic Alu insertions. Proc Natl Acad Sci USA 91:12288-12292
7. Bowcock AM, Kidd JR, Mountain JL, Hebert JM, Carotenuto L, Kidd KK, Cavalli-Sforza LL (1991) Drift, admixture, and selection in human evolution: a study with DNA polymorphisms. Proc Natl Acad Sci USA 88:839-843
8. Bowcock AM, Ruiz-Linares A, Tomfohrde J, Minch E, Kidd JR, Cavalli-Sforza LL (1994) High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368:455-457
9. Calafell F, Shuster A, Speed WC, Kidd JR, Kidd KK (1998) Short tandem repeat polymorphism evolution in humans. Eur J Hum Genet 6:38-49
10. Cavalli-Sforza LL (1998) The DNA revolution in population genetics. Trends Genet 14:60-65
11. Crouau-Roy B, Service S, Slatkin M, Freimer N (1996) A fine-scale comparison of the human and chimpanzee genomes: linkage, linkage disequilibrium and sequence analysis. Hum Mol Genet 5:1131-1137
12. Deka R, Guangyun S, Smelser D, Zhong Y, Kimmel M, Chakraborty R (1999) Rate and directionality of mutations and effects of allele size constraints at anonymous, gene-associated, and disease-causing trinucleotide loci. Mol Biol Evol 16:1166-1177
13. Deka R, Jin L, Shriver MD, Yu LM, DeCroo S, Hundrieser J, Bunker CH, et al (1995a) Population genetics of dinucleotide (dC-dA)n.(dG-dT)n polymorphisms in world populations. Am J Hum Genet 56:461-474
14. Deka R, Jin L, Shriver MD, Yu LM, Saha N, Barrantes R, Chakraborty R, et al (1996) Dispersion of human Y chromosome haplotypes based on five microsatellites in global populations. Genome Res 6:1177-1184
15. Deka R, Shriver MD, Yu LM, Ferrell RE, Chakraborty R (1995b) Intra- and inter-population diversity at short tandem repeat loci in diverse populations of the world. Electrophoresis 16:1659-1664
16. de Knijff P, Kayser M, Caglia A, Corach D, Fretwell N, Gehrig C, Graziosi G, et al (1997) Chromosome Y microsatellites: population genetic and evolutionary aspects. Int J Legal Med 110:134-140
17. Di Rienzo A, Peterson AC, Garza JC, Valdes AM, Slatkin M, Freimer NB (1994) Mutational processes of simple-sequence repeat loci in human populations. Proc Natl Acad Sci USA 91:3166-3170
18. Excoffier L, Smouse PE, Quattro JM (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479-491
19. Fay JC, Wu C-I (1999) A human population bottleneck can account for the discordance between patterns of mitochon drial versus nuclear DNA variation. Mol Biol Evol 16: 1003-1005
20. Halushka MK, Fan JB, Bentley K, Hsie L, Shen N, Weder A, Cooper R, et al (1999) Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat Genet 22:239-247
21. Hammer MF, Spurdle AB, Karafet T, Bonner MR, Wood ET, Novelletto A, Malaspina P, et al (1997) The geographic distribution of Y chromosome variation. Genetics 145: 787-805
22. Harpending HC, Batzer MA, Gurven M, Jorde LB, Rogers AR, Sherry ST (1998) Genetic traces of ancient demography. Proc Natl Acad Sci USA 95:1961-1967
23. Harris EE, Hey J (1999) X chromosome evidence for ancient human histories. Proc Natl Acad Sci USA 96:3320-3324
24. Hey J (1997) Mitochondrial and nuclear genes present conflicting portraits of human origins. Mol Biol Evol 14: 166-172
25. Heyer E, Puymirat J, Dieltjes P, Bakker E, de Knijff P (1997) Estimating Y chromosome specific microsatellite mutation frequencies using deep rooting pedigrees. Hum Mol Genet 6:799-803
26. Jin L, Chakraborty R (1995) Population structure, stepwise mutations, heterozygote deficiency and their implications in DNA forensics. Heredity 74:274-285
27. Jorde LB (1980) The genetic structure of subdivided human populations: a review. In: Mielke JH, Crawford MH (eds) Current developments in anthropological genetics. Vol 1. Plenum Press, New York, pp 135-208
28. Jorde LB, Bamshad M, Rogers AR (1998) Using mitochondrial and nuclear DNA markers to reconstruct human evolution. Bioessays 20:126-136
29. Jorde LB, Bamshad MJ, Watkins WS, Zenger R, Fraley AE, Krakowiak PA, Carpenter KD, et al (1995) Origins and affinities of modern humans: a comparison of mitochondrial and nuclear genetic data. Am J Hum Genet 57:523-538
30. Jorde LB, Rogers AR, Bamshad M, Watkins WS, Krakowiak P, Sung S, Kere J, et al (1997) Microsatellite diversity and the demographic history of modern humans. Proc Natl Acad Sci USA 94:3100-3103
31. Kaessmann H, Heissig F, von Haeseler A, Pääbo S (1999a) DNA sequence variation in a non-coding region of low recombination on the human X chromosome. Nat Genet 22: 78-81
32. Kaessmann H, Wiebe V, Pääbo S (1999b) Extensive nuclear DNA sequence diversity among chimpanzees. Science 286: 1159-1162
33. Kayser M, Caglia A, Corach D, Fretwell N, Gehrig C, Graziosi G, Heidorn F, et al (1997) Evaluation of Y-chromosomal STRs: a multicenter study. Int J Legal Med 110:125-133, 141-149
34. Kimmel M, Chakraborty R, King JP, Bamshad M, Watkins WS, Jorde LB (1998) Signatures of population expansion in microsatellite repeat data. Genetics 148:1921-1930
35. Kittles RA, Bergen AW, Urbanek M, Virkkunen M, Linnoila M, Goldman D, Long JC (1999) Autosomal, mitochondrial, and Y chromosome DNA variation in Finland: evidence for a male-specific bottleneck. Am J Phys Anthropol 108: 381-399
36. Lewontin RC (1972) The apportionment of human diversity. Evol Biol 6:381-398
37. Li W-H, Sadler LA (1991) Low nucleotide diversity in man. Genetics 129:513-523
38. Lum JK, Cann RL, Martinson JJ, Jorde LB (1998) Mitochondrial and nuclear genetic relationships among Pacific Island and Asian populations. Am J Hum Genet 63: 613-624
39. Merriwether DA, Clark AG, Ballinger SW, Schurr TG, Soodyall H, Jenkins T, Sherry ST, et al (1991) The structure of human mitochondrial DNA variation. J Mol Evol 33: 543-555
40. Merriwether DA, Huston S, Iyengar S, Hamman R, Norris JM, Shetterly SM, Kamboh MI, et al (1997) Mitochondrial versus nuclear admixture estimates demonstrate a past history of directional mating. Am J Phys Anthropol 102: 153-159
41. Meyer S, Weiss G, von Haeseler A (1999) Pattern of nucleotide substitution and rate heterogeneity in the hypervariable regions I and II of human mtDNA. Genetics 152:1103-1110
42. Milewicz DM, Byers PH, Reveille J, Hughes AL, Duvic M (1996) A dimorphic Alu Sb-like insertion in COL3A1 is ethnic-specific. J Mol Evol 42:117-123
43. Mountain JL, Cavalli-Sforza LL (1994) Inference of human evolution through cladistic analysis of nuclear DNA restriction polymorphisms. Proc Natl Acad Sci USA 91:6515-6519
44. National Research Council (1996) The evaluation of forensic DNA evidence. National Academy Press, Washington, DC
45. Nei M, Livshits G (1990) Evolutionary relationships of Europeans, Asians, and Africans at the molecular level. In: Takahata N, Crow JF (eds) Population biology of genes and molecules. Baifukan, Tokyo, pp 251-265
46. Nei M, Livshits G, Ota T (1993) Genetic variation and evolution of human populations. In: Sing CF, Hanis CL (eds) Genetics of cellular, individual, family, and population variability. Oxford University Press, New York, pp 239-252
47. Nickerson DA, TayJor SL, Weiss KM, Clark AG, Hutchinson RG, Stengard J, Salomaa V, et al (1998) DNA sequence diversity in a 9.7-kb region of the human lipoprotein lipase gene. Nat Genet 19:233-240
48. Passarino G, Semino O, Quintana-Murci L, Excoffier L, Hammer M, Santachiara-Benerecetti AS (1998) Different genetic components in the Ethiopian population, identified by mtDNA and Y-chromosome polymorphisms. Am J Hum Genet 62:420-434
49. Perez-Lezaun A, Calafell F, Comas D, Mateu E, Bosch E, Martinez-Arias R, Clarimon J, et al (1999) Sex-specific migration patterns in Central Asian populations, revealed by analysis of Y-chromosome short tandem repeats and mtDNA. Am J Hum Genet 65:208-219
50. Poloni ES, Semino O, Passarino G, Santachiara-Beneceretti AS, Dupanloup I, Langaney A, Excoffier L (1997) Human genetic affinities for Y-chromosome P49a,f/TaqI haplotypes show strong correspondence with linguistics. Am J Hum Genet 61:1015-1035
51. Quintana-Murci L, Semino O, Poloni ES, Liu A, Van Gijn M, Passarino G, Brega A, et al (1999) Y-chromosome specific YCAII, DYS19 and YAP polymorphisms in human populations: a comparative study. Ann Hum Genet 63: 153-166
52. Reich DE, Goldstein DB (1998) Genetic evidence for a Paleolithic human population expansion in Africa. Proc Natl Acad Sci USA 95:8119-8123
53. Relethford JH (1995) Genetics and modern human origins. Evol Anthropol 4:53-63
54. Relethford JH, Harpending HC (1994) Craniometric variation, genetic theory, and modern human origins. Am J Phys Anthropol 95:249-270
55. Relethford JH, Jorde LB (1999) Genetic evidence for larger African population size during recent human evolution. Am J Phys Anthropol 108:251-260
56. Rieder MJ, Taylor SL, Clark AG, Nickerson DA (1999) Sequence variation in the human angiotensin converting enzyme. Nat Genet 22:59-62
57. Rogers AR (1995) Genetic evidence for a Pleistocene population explosion. Evolution 49:608-615
58. Rogers AR, Jorde LB (1995) Genetic evidence on the origin of modern humans. Hum Biol 67:1-36
59. _ (1996) Ascertainment bias in estimates of average heterozygosity. Am J Hum Genet 58:1033-1041
60. Sajantila A, Salem A, Savolainen P, Bauer K, Gierig C, Pääbo S (1996) Paternal and maternal DNA lineages reveal a bottleneck in the founding of the Finnish population. Proc Natl Acad Sci USA 93:12035-12039
61. Schneider S, Kueffer J-M, Roesslie D, Excoffier L (1997) Arlequin, version 1.1: a software for population genetic data analysis. Genetics and Biometry Laboratory, University of Geneva, Geneva
62. Scozzari R, Cruciani F, Malaspina P, Santolamazza P, Ciminelli BM, Torroni A, Modiano D, et al (1997) Differential structuring of human populations for homologous X and Y microsatellite loci. Am J Hum Genet 61:719-733
63. Seielstad M, Bekele D, Ibrahim M, Touré A, Traoré M (1999) A view of modem human origins from Y chromosome microsatellite variation. Genome Res 9:558-567
64. Seielstad MT, Minch E, Cavalli-Sforza LL (1998) Genetic evidence for a higher female migration rate in humans. Nat Genet 20:278-280
65. Shriver MD, Jin L, Boerwinkle E, Deka R, Ferrell RE, Chakraborty R (1995) A novel measure of genetic distance for highly polymorphic tandem repeat loci. Mol Biol Evol 12: 914-920
66. Shriver MD, Jin L, Ferrell RE, Deka R (1997) Microsatellite data support an early population expansion in Africa. Genome Res 7:586-591
67. Spurdle AB, Jenkins T (1996) The origins of the Lemba "Black Jews" of southern Africa: evidence from p12F2 and other Y-chromosome markers. Am J Hum Genet 59: 1126-1133
68. Stoneking M (1993) DNA and recent human evolution. Evol Anthropol 2:60-73
69. Stoneking M, Fontius JJ, Clifford SL, Soodyall H, Arcot SS, Saha N, Jenkins T, et al (1997) Alu insertion polymorphisms and human evolution: evidence for a larger population size in Africa. Genome Res 7:1061-1071
70. Stoneking M, Jorde LB, Bhatia K, Wilson AC (1990) Geographic variation of human mitochondrial DNA from Papua New Guinea. Genetics 124:717-733
71. Urbanek M, Goldman D, Long JC (1996) The apportionment of dinucleotide diversity in Native Americans and Europeans: a new approach to measuring gene identity reveals asymmetric patterns of divergence. Mol Biol Evol 13: 943-953
72. Vigilant L, Stoneking M, Harpending H, Hawkes K, Wilson AC (1991) African populations and the evolution of human mitochondrial DNA. Science 253:1503-1507
73. Watkins WS, Bamshad MJ, Jorde LB (1995) Population genetics of trinucleotide repeat polymorphisms. Hum Mol Genet 4:1485-1491
74. Wright S (1965) The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution 19:395-420
75. Zietkiewicz E, Yotova V, Jarnik M, Korab-Laskowska M, Kidd KK, Modiano D, Scozzari R, et al (1998) Genetic structure of the ancestral population of modern humans. J Mol Evol 47:146-155